[Pw_forum] pw.x running but nothing happens

wangqj1 wangqj1 at 126.com
Mon Sep 7 08:55:30 CEST 2009 

Dear Lorenzo
I now use 16 CPUs(2 nodes) to run the task ,the job runs but very slower than use 4 CPUs in my personal computer ,I use top to look CPU information,it as following:
 
Tasks: 176 total,   1 running, 175 sleeping,   0 stopped,   0 zombie
Cpu0  :  0.4%us,  0.4%sy,  0.0%ni, 99.3%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu1  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu2  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu3  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu4  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu5  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu6  :  0.7%us,  0.0%sy,  0.0%ni, 99.3%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu7  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:   8048812k total,  5537848k used,  2510964k free,   315448k buffers
Swap:  4192956k total,        0k used,  4192956k free,  5022856k cached

Why only display 8 CPUs information and the usage of CPU is so small ? 
 
Best regards
Q.J.Wang
XiangTan University




在2009-09-07?02:05:35，pw_forum-request at pwscf.org?写道：
>Send?Pw_forum?mailing?list?submissions?to
>	pw_forum at pwscf.org
>
>To?subscribe?or?unsubscribe?via?the?World?Wide?Web,?visit
>	http://www.democritos.it/mailman/listinfo/pw_forum
>or,?via?email,?send?a?message?with?subject?or?body?'help'?to
>	pw_forum-request at pwscf.org
>
>You?can?reach?the?person?managing?the?list?at
>	pw_forum-owner at pwscf.org
>
>When?replying,?please?edit?your?Subject?line?so?it?is?more?specific
>than?"Re:?Contents?of?Pw_forum?digest..."
>
>
>Today's?Topics:
>
>???1.?Re:?pw.x?running?but?nothing?happens?(Bipul?Rakshit)
>???2.?pseudo?potential?(Mansoureh?Pashangpour)
>???3.?Re:?error?loading?shared?libraries?on?parallel?execution
>??????(Paolo?Giannozzi)
>???4.?Re:?pw.x?running?but?nothing?happens?(Lorenzo?Paulatto)
>???5.?Re:?Pw_forum?Digest,?Vol?27,?Issue?23?(sreekar?guddeti)
>
>
>----------------------------------------------------------------------
>
>Message:?1
>Date:?Sun,?6?Sep?2009?08:03:29?+0100
>From:?Bipul?Rakshit?<bipulrr at gmail.com>
>Subject:?Re:?[Pw_forum]?pw.x?running?but?nothing?happens
>To:?PWSCF?Forum?<pw_forum at pwscf.org>
>Message-ID:
>	<3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com>
>Content-Type:?text/plain;?charset="gb2312"
>
>Dear?Wangqj,
>The?same?thing?happens?to?me.
>since?you?are?using?large?no.?of?wfc,?although?it?shows?the?job?is?running
>in?8?procs,?but?sometimes?if?the?installation?is?not?proper,?it?is?running
>in?1?procs?only.
>
>So?better?you?check?the?parallel?installation?using?a?small?job,?with
>different?no.?of?procs?and?see?whether?its?taking?lesser?time?as??no.?of
>procs?increases?or?not?
>
>cheers
>
>2009/9/6?wangqj1?<wangqj1 at 126.com>
>
>>
>>?Dear?pwscf?users
>>??????When?I?run?vc-relax?on?the?computing?cluster?use?one?node?which?has?8
>>?CPUs.
>>?The?output?file?is?as?following:
>>
>>?Program?PWSCF?????v.4.0.1??starts?...
>>??????Today?is??6Sep2009?at??7:49:30
>>??????Parallel?version?(MPI)
>>??????Number?of?processors?in?use:???????8
>>??????R?&?G?space?division:??proc/pool?=????8
>>??????For?Norm-Conserving?or?Ultrasoft?(Vanderbilt)?Pseudopotentials?or?PAW
>>?.....................................................................
>>??????Initial?potential?from?superposition?of?free?atoms
>>??????starting?charge??435.99565,?renormalised?to??436.00000
>>??????Starting?wfc?are??254?atomic?+????8?random?wfc
>>
>>?After?one?day?,it?still?like?this?and?no?iteration?has?completed?,there?is
>>?also?no?error?was?turn?up?.There?is?no?error?in?the?input?file?because?I
>>?have?test?it?on?anthoer?computer?which?has?4?CPUs?and?it?runs?well?.
>>?I?can't?find?the?reason?about?this?,any?help?will?be?appreciated?.
>>?Best?Regards
>>?Q.J.Wang
>>?XiangTan?University
>>
>>
>>
>>?------------------------------
>>????????????,www.yeah.net?<http://www.yeah.net/?from=footer>
>>?_______________________________________________
>>?Pw_forum?mailing?list
>>?Pw_forum at pwscf.org
>>?http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
>--?
>Dr.?Bipul?Rakshit
>Research?Associate,
>S?N?Bose?Centre?for?Basic?Sciences,
>Salt?Lake,
>Kolkata?700?098
>India
>--------------?next?part?--------------
>An?HTML?attachment?was?scrubbed...
>URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm?
>
>------------------------------
>
>Message:?2
>Date:?Sun,?6?Sep?2009?11:25:06?+0330
>From:?Mansoureh?Pashangpour?<mansourehp at gmail.com>
>Subject:?[Pw_forum]?pseudo?potential
>To:?PWSCF?Forum?<pw_forum at pwscf.org>
>Message-ID:
>	<cbe1626b0909060055o66690789yc0ae02efdfa5391e at mail.gmail.com>
>Content-Type:?text/plain;?charset="iso-8859-1"
>
>Dear?all
>how?can?I??plot?these?pseudo?potentials??how?can?I?discribe?the?properties
>of?pseudo?potentials?
>
>*Fe.pbe-nd-rrkjus.UPF*<http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF>
>?(
>*details*<http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF>)
>
>
>	?Perdew-Burke-Ernzerhof?(PBE)?exch-corr
>	?nonlinear?core-correction
>	?semicore?state?d?in?valence
>	?Rabe?Rappe?Kaxiras?Joannopoulos?(ultrasoft)
>
>and
>
>*H.pbe-rrkjus.UPF*?<http://www.pwscf.org/pseudo/1.3/UPF/H.pbe-rrkjus.UPF>
>(*details*?<http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF>)
>
>
>	?Perdew-Burke-Ernzerhof?(PBE)?exch-corr
>	?Rabe?Rappe?Kaxiras?Joannopoulos?(ultrasoft)
>
>
>and
>
>*O.pbe-rrkjus.UPF*
><http://www.pwscf.org/pseudo/1.3/UPF/O.pbe-rrkjus.UPF>???(*details*
><http://www.pwscf.org/pseudo/upfdetails.php?upf=O.pbe-rrkjus.UPF>)
>
>	?Perdew-Burke-Ernzerhof?(PBE)?exch-corr
>	?Rabe?Rappe?Kaxiras?Joannopoulos?(ultrasoft)
>
>
>Thanks
>Mansoureh?Pashangpour
>Ph.D?student
>Islami?Azad?university
>science?&?reaserch?branch
>Tehran,?IRAN
>--------------?next?part?--------------
>An?HTML?attachment?was?scrubbed...
>URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm?
>
>------------------------------
>
>Message:?3
>Date:?Sun,?6?Sep?2009?10:24:48?+0200
>From:?Paolo?Giannozzi?<giannozz at democritos.it>
>Subject:?Re:?[Pw_forum]?error?loading?shared?libraries?on?parallel
>	execution
>To:?PWSCF?Forum?<pw_forum at pwscf.org>
>Message-ID:?<E6918F77-0C97-4F26-9F7E-BE790E9EFC6B at democritos.it>
>Content-Type:?text/plain;?charset=US-ASCII;?format=flowed
>
>
>On?Sep?6,?2009,?at?1:20?,?sreekar?guddeti?wrote:
>
>>?plz?suggest?solutions?which?donot?require?root?permissions?,
>>?as?i?dont?have
>
>somebody?must?have?it.?Report?the?problem?and?the
>solution??(i.e.?install?gfortran?on?ALL?processors)?to
>whoever?has?root?access.?As?an?alternative,?try?static
>link?(add?-static?to?LDFLAGS?in?make.sys).
>---
>Paolo?Giannozzi,?Dept?of?Physics,?University?of?Udine
>via?delle?Scienze?208,?33100?Udine,?Italy
>Phone?+39-0432-558216,?fax?+39-0432-558222
>
>
>
>
>
>------------------------------
>
>Message:?4
>Date:?Sun,?6?Sep?2009?12:20:40?+0200?(CEST)
>From:?"Lorenzo?Paulatto"?<paulatto at sissa.it>
>Subject:?Re:?[Pw_forum]?pw.x?running?but?nothing?happens
>To:?"PWSCF?Forum"?<pw_forum at pwscf.org>
>Message-ID:?<46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it>
>Content-Type:?text/plain;charset=iso-8859-1
>
>
>On?Sun,?September?6,?2009?02:33,?wangqj1?wrote:
>>??After?one?day?,it?still?like?this?and?no?iteration?has?completed?,there
>>??is
>>??also?no?error?was?turn?up?.There?is?no?error?in?the?input?file?because?I
>>??have?test?it?on?anthoer?computer?which?has?4?CPUs?and?it?runs?well?.
>>??I?can't?find?the?reason?about?this?,any?help?will?be?appreciated?.
>
>
>Dear?QJ,
>this?is?strange.?But?we?would?need?more?information?on?your?hardwre
>configuration?in?order?to?help?you.?In?the?mean?while?you?can?check?the
>behaviour?of?te?pw.x?processes?with?"top".?E.g.?if?they?are?all?runing?at
>100%?CPU,?how?much?memory?they?are?taking?and?so?on.
>
>regards
>
>
>--?
>Lorenzo?Paulatto
>SISSA??&??DEMOCRITOS?(Trieste)
>phone:?+39?040?3787?511
>skype:?paulatz
>www:???http://people.sissa.it/~paulatto/
>
>
>
>----------------------------------------------------------------
>??SISSA?Webmail?https://webmail.sissa.it/
>??Powered?by?SquirrelMail?http://www.squirrelmail.org/
>
>
>
>------------------------------
>
>Message:?5
>Date:?Sun,?6?Sep?2009?23:35:26?+0530
>From:?sreekar?guddeti?<colonel.sreekar at gmail.com>
>Subject:?Re:?[Pw_forum]?Pw_forum?Digest,?Vol?27,?Issue?23
>To:?pw_forum at pwscf.org
>Message-ID:
>	<c864e4460909061105i43b1885dh6141b2789b8ae51 at mail.gmail.com>
>Content-Type:?text/plain;?charset="iso-8859-1"
>
>@duy?lee
>i?inserted?the?line?#$?-V?in?my?qsub?script?and?the?env?variable
>$LD_LIBRARY_PATH?is?being?set?from?script...?thanks?for?that?but?still
>problem?persists.
>
>@rakshit
>
>-----------------------------
>$find?/usr/lib?-name?libgfortran*
>-----------------------------
>and?output?is
>_______________________
>/usr/lib/libgfortran.so.1.0.0
>/usr/lib/libgfortran.so.1
>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a
>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a
>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so
>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a
>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a
>/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so
>_______________________
>whereas?on?doing
>-----------------------------
>$find?/usr/lib64?-name?libgfortran*
>-----------------------------
>ouput?is
>_________________
>/usr/lib64/libgfortran.so.3.0.0
>/usr/lib64/libgfortran.so.1.0.0
>/usr/lib64/libgfortran.so.1
>find:?/usr/lib64/audit:?Permission?denied
>*/usr/lib64/libgfortran.so.3*
>_________________
>
>it?means?my?OS?has?the?required?library,?i?guess
>
>i?installed?the?QE?on?the?head?node
>This?cluster?is?a?Rocks?cluster?with
>
>???#?of?nodes:?10?(1?head?node?+?9?compute?nodes)
>???#?of?processors/node:?8
>???#?Total?#?of?processors:?10X8?=?80
>
>i?tested?the?sample?program?for?submitting?batch?jobs?using?SGE?utility?and
>it?is?working?fine(
>http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html)
>
>sincerely,
>sreekar?guddeti
>Dept.?Physics
>IIT?Bombay
>India
>
>
>On?Sun,?Sep?6,?2009?at?12:28?PM,?<pw_forum-request at pwscf.org>?wrote:
>
>>?Send?Pw_forum?mailing?list?submissions?to
>>????????pw_forum at pwscf.org
>>
>>?To?subscribe?or?unsubscribe?via?the?World?Wide?Web,?visit
>>????????http://www.democritos.it/mailman/listinfo/pw_forum
>>?or,?via?email,?send?a?message?with?subject?or?body?'help'?to
>>????????pw_forum-request at pwscf.org
>>
>>?You?can?reach?the?person?managing?the?list?at
>>????????pw_forum-owner at pwscf.org
>>
>>?When?replying,?please?edit?your?Subject?line?so?it?is?more?specific
>>?than?"Re:?Contents?of?Pw_forum?digest..."
>>
>>
>>?Today's?Topics:
>>
>>???1.?Re:?error?loading?shared?libraries?on?parallel?execution?(Duy?Le)
>>???2.?pw.x?running?but?nothing?happens?(wangqj1)
>>???3.?Re:?error?loading?shared?libraries?on?parallel?execution
>>??????(Bipul?Rakshit)
>>
>>
>>?----------------------------------------------------------------------
>>
>>?Message:?1
>>?Date:?Sat,?5?Sep?2009?19:39:17?-0400
>>?From:?Duy?Le?<ttduyle at gmail.com>
>>?Subject:?Re:?[Pw_forum]?error?loading?shared?libraries?on?parallel
>>????????execution
>>?To:?PWSCF?Forum?<pw_forum at pwscf.org>
>>?Message-ID:
>>????????<8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com>
>>?Content-Type:?text/plain;?charset="iso-8859-1"
>>
>>?Hi,I?am?not?sure?if?this?help.?Could?you?please?try?to?add
>>?#$?-V?in?your?submitting?script.?Like?this:
>>
>>?#!/bin/bash
>>?#
>>?#$?-V
>>?#$?-cwd
>>?#$?-j?y
>>?#$?-S?/bin/bash
>>?#
>>
>>?Good?luck.
>>?D.
>>
>>?On?Sat,?Sep?5,?2009?at?7:20?PM,?sreekar?guddeti
>>?<colonel.sreekar at gmail.com>wrote:
>>
>>?>?i?know?this?issuehas?been?addressed?and?documented?in?troubleshooting
>>?>?section?of?the?users?guide.
>>?>?but?i?giveup?in?despair?trying?for?a?whole?day?to?figure?this?problem
>>?>?i?run?my?jobs?on?rocks?cluster?by?using?SGE's?facility?of?submitting
>>?batch
>>?>?jobs
>>?>
>>?>
>>?http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html
>>?>
>>?>?what?i?'apparently'?observe(or?doubtfully?infer)?is?that?i?can
>>?successfully
>>?>?run?a?single?parallel?job,?but?on?submitting?a?second?job?i?get?the?error
>>?>?____________________________________________
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?____________________________________________
>>?>
>>?>
>>?>?i?find?out?the?path?for?the?library?and?added?to?the?LD_LIBRARY_PATH?by
>>?>?writing
>>?>?_______________________________________
>>?>?#set?the?library?path?to?include?gfortran?libraries
>>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
>>?>
>>?>
>>?>?$ECHO
>>?>?$ECHO?"$LD_LIBRARY_PATH"
>>?>?$ECHO
>>?>?_______________________________________
>>?>
>>?>?in?the?file?which?acts?as?script?for?qsub?($qsub?-pe?orte?4
>>?>?dosroutine.qsub)?which?is
>>?>
>>?>?dosroutine.qsub
>>?>?-----------------------------------------------------------------
>>?>
>>?>?#!/bin/bash
>>?>?#
>>?>?#$?-cwd
>>?>?#$?-j?y
>>?>?#$?-S?/bin/bash
>>?>?#
>>?>
>>?>?#extract?the?info?about?no?of?processors?involved?from?command?line
>>?>?arguments?of?'qsub'
>>?>?PROCESSORS=$NSLOTS
>>?>
>>?>?#heuristically?assign?the?no?of?processors?per?pool?NPR
>>?>?NPR=4
>>?>?#as?a?result?no?of?pools?are?give?by
>>?>?NPK=`expr?$PROCESSORS?/?$NPR`
>>?>
>>?>?#!/bin/bash
>>?>?#
>>?>?#
>>?>?#Script?for?performing?a?dos?calculation?on?a?parallel?processor
>>?>?WORKINGDIR=`pwd`
>>?>?ECHO="echo"
>>?>
>>?>?#set?the?library?path?to?include?gfortran?libraries
>>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
>>?>
>>?>
>>?>?$ECHO
>>?>?$ECHO?"$LD_LIBRARY_PATH"
>>?>?$ECHO
>>?>
>>?>?#?set?the?needed?environment?variables
>>?>
>>?>?PREFIX=`cd?/home3/colonel/espresso-4.0.5?;?pwd`
>>?>?$ECHO?$PREFIX
>>?>?BIN_DIR=$PREFIX/bin
>>?>?PSEUDO_DIR=$PREFIX/pseudo
>>?>?TMP_DIR=$HOME/tmp
>>?>?PARA_PREFIX="/opt/openmpi/bin/mpirun?-np?$PROCESSORS"
>>?>?PARA_POSTFIX="-npool?$NPK"
>>?>
>>?>?#?required?executables?and?pseudopotentials
>>?>?$ECHO
>>?>?$ECHO?"??executables?directory:?$BIN_DIR"
>>?>?$ECHO?"??pseudo?directory:??????$PSEUDO_DIR"
>>?>?$ECHO?"??temporary?directory:???$TMP_DIR"
>>?>
>>?>?#create?results?directory
>>?>?for?DIR?in?"$TMP_DIR"?"$WORKINGDIR/results"?;?do
>>?>?????if?test?!?-d?$DIR?;?then
>>?>?????????mkdir?$DIR
>>?>?????fi
>>?>?done
>>?>?cd?$WORKINGDIR/results
>>?>
>>?>
>>?>?#?variables?to?represent?programs
>>?>?PW_COMMAND="$PARA_PREFIX?$BIN_DIR/pw.x?$PARA_POSTFIX"
>>?>?DOS_COMMAND="$PARA_PREFIX?$BIN_DIR/dos.x?$PARA_POSTFIX"
>>?>?PROJWFC_COMMAND="$PARA_PREFIX?$BIN_DIR/projwfc.x?$PARA_POSTFIX"
>>?>
>>?>
>>?>?#?DOS?calculation?for?0Ni0
>>?>?cat?>?0ni0.dos.in?<<?EOF
>>?>??&control
>>?>?????calculation='nscf'
>>?>?????restart_mode='from_scratch',
>>?>?????prefix='0ni0',
>>?>?????pseudo_dir?=?'$PSEUDO_DIR/',
>>?>?????outdir='$TMP_DIR/'
>>?>??/
>>?>??&system
>>?>?????ibrav=2,?celldm(1)?=6.48,?nat=1,?ntyp=1,
>>?>?????nspin?=?2,??starting_magnetization(1)=0.7,
>>?>?????ecutwfc?=?24.0,?ecutrho?=?288.0,?nbnd=8,
>>?>?????occupations='tetrahedra'
>>?>??/
>>?>??&electrons
>>?>?????conv_thr?=?1.0e-10
>>?>?????mixing_beta?=?0.7
>>?>??/
>>?>?ATOMIC_SPECIES
>>?>??Ni?58.69?NiUS.RRKJ3.UPF
>>?>?ATOMIC_POSITIONS
>>?>??Ni?0.0?0.0?0.0
>>?>?K_POINTS?{automatic}????????!special?points?generated?by?tetrahedra
>>?method
>>?>??12?12?12?0?0?0
>>?>?EOF
>>?>
>>?>?$ECHO?"??running?DOS?calculation?for?0Ni0?...\c"
>>?>?$PW_COMMAND?<?0ni0.dos.in?>?0ni0.dos.out
>>?>?$ECHO
>>?>?$ECHO?"???done"
>>?>
>>?>?-------------------------------------------------------------
>>?>
>>?>?the?output?i?get?is
>>?>
>>?>?************************************************
>>?>?:/usr/lib64:/usr/lib
>>?>
>>?>?/home3/colonel/espresso-4.0.5
>>?>
>>?>???executables?directory:?/home3/colonel/espresso-4.0.5/bin
>>?>???pseudo?directory:?????/home3/colonel/espresso-4.0.5/pseudo
>>?>???temporary?directory:???/home3/colonel/tmp
>>?>???running?DOS?calculation?for?0Ni0?...\c
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>
>>?>????done
>>?>?*************************************************
>>?>?plz?suggest?solutions?which?donot?require?root?permissions?,?as?i?dont
>>?have
>>?>?thanks?in?advance
>>?>?--
>>?>?Sreekar?Guddeti
>>?>?Department?of?Physics
>>?>
>>?>?_______________________________________________
>>?>?Pw_forum?mailing?list
>>?>?Pw_forum at pwscf.org
>>?>?http://www.democritos.it/mailman/listinfo/pw_forum
>>?>
>>?>
>>
>>
>>?--
>>?--------------------------------------------------
>>?Duy?Le
>>?PhD?Student
>>?Department?of?Physics
>>?University?of?Central?Florida.
>>?--------------?next?part?--------------
>>?An?HTML?attachment?was?scrubbed...
>>?URL:
>>?http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm
>>
>>?------------------------------
>>
>>?Message:?2
>>?Date:?Sun,?6?Sep?2009?08:33:25?+0800?(CST)
>>?From:?wangqj1?<wangqj1 at 126.com>
>>?Subject:?[Pw_forum]?pw.x?running?but?nothing?happens
>>?To:?pw_forum?<pw_forum at pwscf.org>
>>?Message-ID:
>>????????<25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com>
>>?Content-Type:?text/plain;?charset="gbk"
>>
>>
>>?Dear?pwscf?users
>>?????When?I?run?vc-relax?on?the?computing?cluster?use?one?node?which?has?8
>>?CPUs.
>>?The?output?file?is?as?following:
>>
>>?Program?PWSCF?????v.4.0.1??starts?...
>>?????Today?is??6Sep2009?at??7:49:30
>>?????Parallel?version?(MPI)
>>?????Number?of?processors?in?use:???????8
>>?????R?&?G?space?division:??proc/pool?=????8
>>?????For?Norm-Conserving?or?Ultrasoft?(Vanderbilt)?Pseudopotentials?or?PAW
>>?.....................................................................
>>?????Initial?potential?from?superposition?of?free?atoms
>>?????starting?charge??435.99565,?renormalised?to??436.00000
>>?????Starting?wfc?are??254?atomic?+????8?random?wfc
>>
>>?After?one?day?,it?still?like?this?and?no?iteration?has?completed?,there?is
>>?also?no?error?was?turn?up?.There?is?no?error?in?the?input?file?because?I
>>?have?test?it?on?anthoer?computer?which?has?4?CPUs?and?it?runs?well?.
>>?I?can't?find?the?reason?about?this?,any?help?will?be?appreciated?.
>>?Best?Regards
>>?Q.J.Wang
>>?XiangTan?University
>>
>>?--------------?next?part?--------------
>>?An?HTML?attachment?was?scrubbed...
>>?URL:
>>?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm
>>
>>?------------------------------
>>
>>?Message:?3
>>?Date:?Sun,?6?Sep?2009?07:58:49?+0100
>>?From:?Bipul?Rakshit?<bipulrr at gmail.com>
>>?Subject:?Re:?[Pw_forum]?error?loading?shared?libraries?on?parallel
>>????????execution
>>?To:?PWSCF?Forum?<pw_forum at pwscf.org>
>>?Message-ID:?<3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com>
>>?Content-Type:?text/plain;?charset="iso-8859-1"
>>
>>?hi,
>>?Just?from?root?user?type
>>?yum?install?libgfortran.so.3
>>
>>?then?it?will?install?this?files?which?is?not?present?in?your?machine
>>
>>?On?Sun,?Sep?6,?2009?at?12:20?AM,?sreekar?guddeti
>>?<colonel.sreekar at gmail.com>wrote:
>>
>>?>?i?know?this?issuehas?been?addressed?and?documented?in?troubleshooting
>>?>?section?of?the?users?guide.
>>?>?but?i?giveup?in?despair?trying?for?a?whole?day?to?figure?this?problem
>>?>?i?run?my?jobs?on?rocks?cluster?by?using?SGE's?facility?of?submitting
>>?batch
>>?>?jobs
>>?>
>>?>
>>?http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html
>>?>
>>?>?what?i?'apparently'?observe(or?doubtfully?infer)?is?that?i?can
>>?successfully
>>?>?run?a?single?parallel?job,?but?on?submitting?a?second?job?i?get?the?error
>>?>?____________________________________________
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?____________________________________________
>>?>
>>?>
>>?>?i?find?out?the?path?for?the?library?and?added?to?the?LD_LIBRARY_PATH?by
>>?>?writing
>>?>?_______________________________________
>>?>?#set?the?library?path?to?include?gfortran?libraries
>>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
>>?>
>>?>
>>?>?$ECHO
>>?>?$ECHO?"$LD_LIBRARY_PATH"
>>?>?$ECHO
>>?>?_______________________________________
>>?>
>>?>?in?the?file?which?acts?as?script?for?qsub?($qsub?-pe?orte?4
>>?>?dosroutine.qsub)?which?is
>>?>
>>?>?dosroutine.qsub
>>?>?-----------------------------------------------------------------
>>?>
>>?>?#!/bin/bash
>>?>?#
>>?>?#$?-cwd
>>?>?#$?-j?y
>>?>?#$?-S?/bin/bash
>>?>?#
>>?>
>>?>?#extract?the?info?about?no?of?processors?involved?from?command?line
>>?>?arguments?of?'qsub'
>>?>?PROCESSORS=$NSLOTS
>>?>
>>?>?#heuristically?assign?the?no?of?processors?per?pool?NPR
>>?>?NPR=4
>>?>?#as?a?result?no?of?pools?are?give?by
>>?>?NPK=`expr?$PROCESSORS?/?$NPR`
>>?>
>>?>?#!/bin/bash
>>?>?#
>>?>?#
>>?>?#Script?for?performing?a?dos?calculation?on?a?parallel?processor
>>?>?WORKINGDIR=`pwd`
>>?>?ECHO="echo"
>>?>
>>?>?#set?the?library?path?to?include?gfortran?libraries
>>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib
>>?>
>>?>
>>?>?$ECHO
>>?>?$ECHO?"$LD_LIBRARY_PATH"
>>?>?$ECHO
>>?>
>>?>?#?set?the?needed?environment?variables
>>?>
>>?>?PREFIX=`cd?/home3/colonel/espresso-4.0.5?;?pwd`
>>?>?$ECHO?$PREFIX
>>?>?BIN_DIR=$PREFIX/bin
>>?>?PSEUDO_DIR=$PREFIX/pseudo
>>?>?TMP_DIR=$HOME/tmp
>>?>?PARA_PREFIX="/opt/openmpi/bin/mpirun?-np?$PROCESSORS"
>>?>?PARA_POSTFIX="-npool?$NPK"
>>?>
>>?>?#?required?executables?and?pseudopotentials
>>?>?$ECHO
>>?>?$ECHO?"??executables?directory:?$BIN_DIR"
>>?>?$ECHO?"??pseudo?directory:??????$PSEUDO_DIR"
>>?>?$ECHO?"??temporary?directory:???$TMP_DIR"
>>?>
>>?>?#create?results?directory
>>?>?for?DIR?in?"$TMP_DIR"?"$WORKINGDIR/results"?;?do
>>?>?????if?test?!?-d?$DIR?;?then
>>?>?????????mkdir?$DIR
>>?>?????fi
>>?>?done
>>?>?cd?$WORKINGDIR/results
>>?>
>>?>
>>?>?#?variables?to?represent?programs
>>?>?PW_COMMAND="$PARA_PREFIX?$BIN_DIR/pw.x?$PARA_POSTFIX"
>>?>?DOS_COMMAND="$PARA_PREFIX?$BIN_DIR/dos.x?$PARA_POSTFIX"
>>?>?PROJWFC_COMMAND="$PARA_PREFIX?$BIN_DIR/projwfc.x?$PARA_POSTFIX"
>>?>
>>?>
>>?>?#?DOS?calculation?for?0Ni0
>>?>?cat?>?0ni0.dos.in?<<?EOF
>>?>??&control
>>?>?????calculation='nscf'
>>?>?????restart_mode='from_scratch',
>>?>?????prefix='0ni0',
>>?>?????pseudo_dir?=?'$PSEUDO_DIR/',
>>?>?????outdir='$TMP_DIR/'
>>?>??/
>>?>??&system
>>?>?????ibrav=2,?celldm(1)?=6.48,?nat=1,?ntyp=1,
>>?>?????nspin?=?2,??starting_magnetization(1)=0.7,
>>?>?????ecutwfc?=?24.0,?ecutrho?=?288.0,?nbnd=8,
>>?>?????occupations='tetrahedra'
>>?>??/
>>?>??&electrons
>>?>?????conv_thr?=?1.0e-10
>>?>?????mixing_beta?=?0.7
>>?>??/
>>?>?ATOMIC_SPECIES
>>?>??Ni?58.69?NiUS.RRKJ3.UPF
>>?>?ATOMIC_POSITIONS
>>?>??Ni?0.0?0.0?0.0
>>?>?K_POINTS?{automatic}????????!special?points?generated?by?tetrahedra
>>?method
>>?>??12?12?12?0?0?0
>>?>?EOF
>>?>
>>?>?$ECHO?"??running?DOS?calculation?for?0Ni0?...\c"
>>?>?$PW_COMMAND?<?0ni0.dos.in?>?0ni0.dos.out
>>?>?$ECHO
>>?>?$ECHO?"???done"
>>?>
>>?>?-------------------------------------------------------------
>>?>
>>?>?the?output?i?get?is
>>?>
>>?>?************************************************
>>?>?:/usr/lib64:/usr/lib
>>?>
>>?>?/home3/colonel/espresso-4.0.5
>>?>
>>?>???executables?directory:?/home3/colonel/espresso-4.0.5/bin
>>?>???pseudo?directory:?????/home3/colonel/espresso-4.0.5/pseudo
>>?>???temporary?directory:???/home3/colonel/tmp
>>?>???running?DOS?calculation?for?0Ni0?...\c
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared
>>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such
>>?>?file?or?directory
>>?>
>>?>????done
>>?>?*************************************************
>>?>?plz?suggest?solutions?which?donot?require?root?permissions?,?as?i?dont
>>?have
>>?>?thanks?in?advance
>>?>?--
>>?>?Sreekar?Guddeti
>>?>?Department?of?Physics
>>?>
>>?>?_______________________________________________
>>?>?Pw_forum?mailing?list
>>?>?Pw_forum at pwscf.org
>>?>?http://www.democritos.it/mailman/listinfo/pw_forum
>>?>
>>?>
>>
>>
>>?--
>>?Dr.?Bipul?Rakshit
>>?Research?Associate,
>>?S?N?Bose?Centre?for?Basic?Sciences,
>>?Salt?Lake,
>>?Kolkata?700?098
>>?India
>>?--------------?next?part?--------------
>>?An?HTML?attachment?was?scrubbed...
>>?URL:
>>?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm
>>
>>?------------------------------
>>
>>?_______________________________________________
>>?Pw_forum?mailing?list
>>?Pw_forum at pwscf.org
>>?http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>?End?of?Pw_forum?Digest,?Vol?27,?Issue?23
>>?****************************************
>>
>
>
>
>--?
>Sreekar?Guddeti
>--------------?next?part?--------------
>An?HTML?attachment?was?scrubbed...
>URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/attachment.htm?
>
>------------------------------
>
>_______________________________________________
>Pw_forum?mailing?list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>End?of?Pw_forum?Digest,?Vol?27,?Issue?24
>****************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20090907/3f73ada9/attachment.html>

More information about the users mailing list